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Zinc in PDB 1tnu: Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob

Enzymatic activity of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob

All present enzymatic activity of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob:
2.5.1.59;

Protein crystallography data

The structure of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob, PDB code: 1tnu was solved by T.S.Reid, K.L.Terry, P.J.Casey, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.94 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 270.359, 266.551, 184.818, 90.00, 131.58, 90.00
R / Rfree (%) 19.3 / 21.2

Other elements in 1tnu:

The structure of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob (pdb code 1tnu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob, PDB code: 1tnu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1tnu

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Zinc binding site 1 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn378

b:54.9
occ:1.00
 NE2 B:HIS321 2.2 52.2 1.0
OD2 B:ASP269 2.3 48.6 1.0
SG B:CYS271 2.3 53.4 1.0
SG M:CYS6 2.3 60.5 1.0
OD1 B:ASP269 2.5 51.9 1.0
CG B:ASP269 2.7 49.3 1.0
CD2 B:HIS321 3.2 50.1 1.0
CE1 B:HIS321 3.2 51.3 1.0
CB B:CYS271 3.4 51.6 1.0
CB M:CYS6 3.5 64.0 1.0
CB B:LYS311 4.2 61.1 1.0
CB B:ASP269 4.2 48.9 1.0
N B:CYS271 4.2 50.5 1.0
ND1 B:HIS321 4.3 50.9 1.0
CG B:HIS321 4.3 51.9 1.0
O B:HOH415 4.3 59.3 1.0
CA B:CYS271 4.4 50.9 1.0
CD2 B:LEU320 4.4 43.8 1.0
CE2 B:TYR272 4.6 50.3 1.0
CE B:LYS311 4.7 66.9 1.0
CA M:CYS6 4.8 65.4 1.0
CD2 B:TYR272 4.9 50.1 1.0
CA B:LYS311 4.9 60.1 1.0

Zinc binding site 2 out of 6 in 1tnu

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Zinc binding site 2 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn378

b:54.0
occ:1.00
 NE2 D:HIS321 2.2 48.2 1.0
SG D:CYS271 2.3 47.8 1.0
OD2 D:ASP269 2.3 52.4 1.0
SG N:CYS6 2.4 58.2 1.0
OD1 D:ASP269 2.5 52.4 1.0
CG D:ASP269 2.7 50.6 1.0
CD2 D:HIS321 3.1 47.7 1.0
CE1 D:HIS321 3.1 48.6 1.0
CB D:CYS271 3.3 45.0 1.0
CB N:CYS6 3.6 64.4 1.0
N D:CYS271 4.1 44.8 1.0
CB D:LYS311 4.1 57.7 1.0
CB D:ASP269 4.2 48.7 1.0
ND1 D:HIS321 4.2 49.2 1.0
CG D:HIS321 4.2 48.9 1.0
CA D:CYS271 4.3 45.1 1.0
O D:HOH448 4.4 53.9 1.0
CD2 D:LEU320 4.4 45.4 1.0
CE2 D:TYR272 4.6 51.8 1.0
CE D:LYS311 4.7 62.5 1.0
CA N:CYS6 4.9 66.8 1.0
CA D:LYS311 4.9 58.0 1.0
CD2 D:TYR272 4.9 50.6 1.0
N N:CYS6 5.0 71.6 1.0

Zinc binding site 3 out of 6 in 1tnu

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Zinc binding site 3 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn378

b:51.3
occ:1.00
 NE2 F:HIS321 2.2 43.6 1.0
SG O:CYS6 2.3 59.9 1.0
OD2 F:ASP269 2.3 43.7 1.0
SG F:CYS271 2.3 45.7 1.0
OD1 F:ASP269 2.5 46.9 1.0
CG F:ASP269 2.7 43.7 1.0
CD2 F:HIS321 3.1 43.8 1.0
CE1 F:HIS321 3.1 45.6 1.0
CB F:CYS271 3.4 41.7 1.0
CB O:CYS6 3.6 63.1 1.0
CB F:LYS311 4.1 56.5 1.0
CB F:ASP269 4.1 44.1 1.0
N F:CYS271 4.2 41.3 1.0
ND1 F:HIS321 4.2 46.3 1.0
CG F:HIS321 4.2 46.8 1.0
O F:HOH444 4.3 44.8 1.0
CA F:CYS271 4.4 42.0 1.0
CD2 F:LEU320 4.4 46.0 1.0
CE2 F:TYR272 4.6 47.2 1.0
CE F:LYS311 4.6 64.4 1.0
CA O:CYS6 4.8 64.7 1.0
CA F:LYS311 4.8 54.8 1.0
CD2 F:TYR272 4.9 47.7 1.0
N O:CYS6 5.0 70.1 1.0

Zinc binding site 4 out of 6 in 1tnu

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Zinc binding site 4 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn378

b:59.8
occ:1.00
 NE2 H:HIS321 2.2 60.2 1.0
OD2 H:ASP269 2.3 49.5 1.0
SG H:CYS271 2.4 54.6 1.0
SG P:CYS6 2.4 67.3 1.0
OD1 H:ASP269 2.5 55.2 1.0
CG H:ASP269 2.7 52.5 1.0
CD2 H:HIS321 3.1 61.0 1.0
CE1 H:HIS321 3.2 60.4 1.0
CB H:CYS271 3.4 54.9 1.0
CB P:CYS6 3.6 71.0 1.0
N H:CYS271 4.1 53.7 1.0
CB H:LYS311 4.1 69.5 1.0
CB H:ASP269 4.1 53.3 1.0
ND1 H:HIS321 4.2 62.4 1.0
CG H:HIS321 4.3 61.4 1.0
CA H:CYS271 4.3 53.5 1.0
CD2 H:LEU320 4.4 52.4 1.0
O H:HOH406 4.4 48.1 1.0
CE2 H:TYR272 4.6 52.1 1.0
CE H:LYS311 4.7 69.3 1.0
CA P:CYS6 4.9 72.3 1.0
CA H:LYS311 4.9 69.4 1.0
CD2 H:TYR272 4.9 52.3 1.0

Zinc binding site 5 out of 6 in 1tnu

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Zinc binding site 5 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn378

b:58.2
occ:1.00
 NE2 J:HIS321 2.2 51.9 1.0
OD2 J:ASP269 2.3 44.0 1.0
SG J:CYS271 2.3 48.6 1.0
SG Q:CYS6 2.4 57.1 1.0
OD1 J:ASP269 2.4 49.3 1.0
CG J:ASP269 2.7 47.6 1.0
CD2 J:HIS321 3.1 50.3 1.0
CE1 J:HIS321 3.2 50.9 1.0
CB J:CYS271 3.4 48.0 1.0
CB Q:CYS6 3.6 62.5 1.0
N J:CYS271 4.1 48.6 1.0
CB J:ASP269 4.1 46.2 1.0
CB J:LYS311 4.1 59.0 1.0
O J:HOH422 4.2 45.3 1.0
ND1 J:HIS321 4.3 51.5 1.0
CG J:HIS321 4.3 50.6 1.0
CA J:CYS271 4.3 48.7 1.0
CD2 J:LEU320 4.4 40.1 1.0
CE2 J:TYR272 4.6 50.2 1.0
CE J:LYS311 4.7 68.3 1.0
CA Q:CYS6 4.9 64.4 1.0
CA J:LYS311 4.9 56.6 1.0
CD2 J:TYR272 4.9 48.6 1.0
N Q:CYS6 5.0 70.3 1.0

Zinc binding site 6 out of 6 in 1tnu

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Zinc binding site 6 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Gcincckvl Peptide Derived From Rhob within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn378

b:50.2
occ:1.00
 NE2 L:HIS321 2.2 40.5 1.0
OD2 L:ASP269 2.2 44.4 1.0
SG L:CYS271 2.3 38.3 1.0
SG R:CYS6 2.3 63.2 1.0
OD1 L:ASP269 2.5 42.4 1.0
CG L:ASP269 2.7 42.3 1.0
CD2 L:HIS321 3.1 41.4 1.0
CE1 L:HIS321 3.2 42.6 1.0
CB L:CYS271 3.4 36.2 1.0
CB R:CYS6 3.6 64.3 1.0
CB L:ASP269 4.1 39.8 1.0
CB L:LYS311 4.1 45.4 1.0
N L:CYS271 4.1 36.9 1.0
ND1 L:HIS321 4.3 44.5 1.0
O L:HOH457 4.3 46.3 1.0
CG L:HIS321 4.3 44.0 1.0
CA L:CYS271 4.4 36.5 1.0
CD2 L:LEU320 4.5 38.0 1.0
CE2 L:TYR272 4.6 39.0 1.0
CE L:LYS311 4.7 57.1 1.0
O L:HOH383 4.8 39.1 1.0
CA R:CYS6 4.9 65.5 1.0
CA L:LYS311 4.9 42.9 1.0
CD2 L:TYR272 4.9 39.8 1.0

Reference:

T.S.Reid, K.L.Terry, P.J.Casey, L.S.Beese. Crystallographic Analysis of Caax Prenyltransferases Complexed with Substrates Defines Rules of Protein Substrate Selectivity. J.Mol.Biol. V. 343 417 2004.
ISSN: ISSN 0022-2836
PubMed: 15451670
DOI: 10.1016/J.JMB.2004.08.056
Page generated: Wed Oct 16 19:12:13 2024

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